MmuINT0023118 @ mm9
Intron Retention
Gene
ENSMUSG00000047617 | BC029214
Description
cDNA sequence BC029214 [Source:MGI Symbol;Acc:MGI:2442831]
Coordinates
chr2:25315295-25315594:-
Coord C1 exon
chr2:25315529-25315594
Coord A exon
chr2:25315380-25315528
Coord C2 exon
chr2:25315295-25315379
Length
149 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
CTGATCCTATTTTCTGGCAGAAC
3' ss Score
8.69
Exon sequences
Seq C1 exon
CTGCAGAAGAGACCATCACTAGCCCCAAGAAGAACACCCAGCCAGCAGGCACTCAGTTCTTACCAG
Seq A exon
GTAAGGGGTGGGCCTGGCATGTGGGCTGGGGCTGCTCTTTCTCTGGAACTGCCTCTCCAGATGTCTCATGGGAGAATCTTTCCATGTGGACAGAGTTCTGGCCAGGGTTCTTTGGAGTTCAAGATTTCCCTGATCCTATTTTCTGGCAG
Seq C2 exon
AACTTGATCACCAGAGAGGCAGCTCTGGGCCTGGGGTCAGGAGACGGTGTCCAGGGGAGTCTCTCATTAACCCTGGCTTCAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000047617-BC029214:NM_153557:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.913 A=NA C2=0.971
Domain overlap (PFAM):
C1:
PF153841=DUF4610=FE(11.2=100)
A:
NA
C2:
PF153841=DUF4610=FE(14.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAGAAGAGACCATCACTAGCC
R:
TTGAAGCCAGGGTTAATGAGAGAC
Band lengths:
146-295
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: